Barrett's esophagus (BE), a sequela of chronic gastroesophageal reflux disease (GERD), is a highly premalignant condition that increases an individual's chance of developing esophageal adenocarcinoma (EAC) by 30- to 125-fold. Therefore, subjects with BE are usually enrolled in surveillance programs in which they undergo endoscopy at regular intervals for the rest of their lives. However, the incidence of EAC in BE patients under surveillance is only 1/200 patient-years. Conversely, cancers or advanced high-grade dysplasias (HGDs) may develop during the interim and are sometimes missed if surveillance is performed at long intervals. In addition, the current marker of EAC risk in BE, dysplasia, is plagued by high inter-observer variability and limited predictive accuracy. Because neoplastic progression is infrequent in BE, the merits of and appropriate interval for endoscopic surveillance in BE have led to frequent debate. Thus, a means of stratifying patients into groups at high, intermediate, and low risk of neoplastic progression would be highly useful. This process would benefit greatly from effective biomarkers to stratify patients according to their level of neoplastic progression risk.
Methylation constitutes the epigenetic modification of DNA by the addition of methyl groups, usually on cytosines at the sequence 5′-CpG-3′. This event is most relevant when it occurs within CpG islands, which are CpG-rich regions in 5′ gene regions of about half of all genes, often involving promoter regions. These islands are normally unmethylated but are vulnerable to de novo methylation, which can silence gene expression. See, e.g., Gardiner-Garden et al. (1987) J Mol Biol 196, 261-282 or Takai et al. (2002) Proc Natl Acad Sci USA 99, 3740-3745 for discussions of CgG islands. It has been reported that promoter hypermethylation of several tumor suppressor genes is correlated with the incidence of several cancers.
The inventors and their colleagues previously reported that hypermethylation of promoter regions of three genes—cyclin-dependent kinase inhibitor 2a (CDKN2a, or p16), runt-related transcription factor 3 (RUNX3), and transmembrane protein with EGF-like and two follistatin-like domains (HPP1)—occurs early in (BE)-associated neoplastic progression and appears to represent independent risk factors for the progression of Barrett's esophagus (BE) to high-grade dysplasias (HGD) or esophageal adenocarcinoma (EAC). See, e.g., Schulmann et al. (2005) Oncogene 24, 4138-4148. Later, the inventors and colleagues developed a tiered risk stratification model to predict progression in BE using epigenetic and clinical features, validating the use of a panel of the three markers (see, e.g., Sato et al. (2008) PLoS ONE 3, e1890).
Hypermethylation of these and additional promoter regions might serve as useful biomarkers for stratifying subjects according to their risk for development of EAC or HGD.